VMD-L Mailing List

From: Tahmina Akter (takter_at_aggies.ncat.edu)
Date: Tue Jul 19 2016 - 11:38:23 CDT

Hello,
I ran some simulation where my system is made up of Si, Au and SiO2. Si is
in bottom and atoms are fixed. On top of the Si, there is Au. On SiO2 there
are some rectangular pillar and I applied pressure and temperature (273) on
SiO2. SiO2 is placed on top of the Au. When I run the simulation, after
some time it shows error message saying
"Periodic cell has become too small for original patch grid". When I ran
the dcd file, I found that Au atoms are flying all around in all the
direction. Any suggestion??

My conf file is

structure combinedTEST.psf
coordinates combinedTEST.pdb

set outputname TEST_NIL
set temperature 273

firsttimestep 0

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid-AU.inp
parameters par_all27_prot_lipid_AU.inp

temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
rigidTolerance 1.0e-8
rigidIterations 100
rigidDieOnError on
useSettle off
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to
#hydrogens

# Periodic Boundary Conditions

cellBasisVector1 120.0 0 0
cellBasisVector2 0 120.0 0
cellBasisVector3 0 0 105.0
cellOrigin -0.72060287 -0.4167399108 6.8767127991

wrapAll on

# PME (for full-system periodic electrostatics)

PME yes
PMEGridSpacing 1.0

#Constant Pressure Control
UseGroupPressure yes
UseFlexibleCell no
UseConstantArea no

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp $temperature

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile combinedTEST_fixed.pdb
fixedAtomsCol B
}

# Output
outputName $outputname

restartfreq 2500 ;# 500steps = every 1ps
dcdfreq 2500
xstFreq 2500
outputEnergies 2500
outputPressure 2500
velDCDfreq 2500

#############################################################
## EXTRA PARAMETERS ##
#############################################################

if {1} {
SMD on
SMDFile combinedTEST_pull.pdb
SMDk 12
SMDVel 0.0005
SMDDir 0 0 -1
SMDOutputFreq 2500
}

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 1000
reinitvels $temperature

run 1250000;#250 ps

Kind regards,
Tahmina Akter